diff --git a/README.md b/README.md index 8463090..78899aa 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,64 @@ # GeneMap +GeneMap, A python tool for identifying the mapping of genes between two genomes by multi evidences. +![Flow chart](https://raw.githubusercontent.com/wjwei-handsome/wwjPic/main/img/20220722001234.png) + +## Table of Contents + +- [Background](#background) +- [Install](#install) +- [Usage](#usage) +- [Badge](#badge) +- [Maintainers](#maintainers) +- [Contributing](#contributing) +- [License](#license) + +## Background + +When we have multiple genomes of the same species (or related species), we usually need to identify the gene mapping relationship between the two genomes(Gene A in genome a, mapped to gene B in genome B). We used four alternative evidence, including: + +1. RBH + **R**eciprocal **B**est BLAST **H**its + + > Despite these and other complication, the identification of reciprocal best hits for gene products is a good first approximation to the identification of orthologues in two or more organisms. It forms the basis for many orthology-finding tools, such as MCL, OrthoMCL and OrthoFinder. It can be carried out by carrying out BLAST+ searches using a short program, and this will be illustrated below. + +2. ortholog + [OrthoFinder](https://github.com/davidemms/OrthoFinder) +3. synteny block + [McScanX]() +4. crosssmap + [minimap](https://github.com/lh3/minimap2) + or + [AnchorWave](https://github.com/baoxingsong/AnchorWave) + +## Install + +TODO + +```sh +$ pip3 install GeneMap +``` + ## Usage -```shell -python3 bin/GeneMap.py -l tests/Zm-B73v5.genelist -d . -q Zm-B73v5 -t Zv-TEO01 +```sh +$ GeneMap.py -l list.txt -d work_dir -q GenomeA -t GenomeB -o output_prefix ``` -![hhh](https://raw.githubusercontent.com/wjwei-handsome/wwjPic/main/img/20220722001234.png) +## Maintainers + +[@wjwei-handsome](https://github.com/wjwei-handsome) + +## Contributing + +Feel free to dive in! [Open an issue](https://github.com/wjwei-handsome/GeneMap/issues/new) or submit PRs. + +Standard Readme follows the [Contributor Covenant](http://contributor-covenant.org/version/1/3/0/) Code of Conduct. + +### Contributors + +Thanks [@songtaogui](https://github.com/songtaogui) for design ideas. + +## License + +[GPL-3.0](LICENSE) © Weiwenjie